Supplementary Table 2B. List of Downregulated and Upregulated Genes Unique to Cyclin D1

Supplementary Table 2A. List of downregulated and upregulated genes in common with both D1 and D3 cyclin knockdown

Probesets / Fold change
D1 siRNA / Fold change
D3 siRNA / Gene Symbol / Gene Name / Entrez Gene / UniGene / SwissProt
220016_at / 0.5 / 0.4 / AHNAK / AHNAK nucleoprotein (desmoyokin) / 79026 / Hs.502756 / Q09666
223006_s_at / 0.5 / 0.5 / C9orf5 / chromosome 9 open reading frame 5 / 23731 / Hs.621479 / Q9H330
239106_at / 0.5 / 0.5 / CA5BL / carbonic anhydrase VB-like / 340591 / Hs.532326 / Q9P170
204256_at / 0.4 / 0.4 / ELOVL6 / ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast) / 79071 / Hs.412939 / Q9H5J4
219895_at / 0.5 / 0.5 / FAM70A / family with sequence similarity 70, member A / 55026 / Hs.437563 / Q5JRV8
242045_at / 0.5 / 0.5 / LOC348840 / hypothetical protein LOC348840 / 348840 / Hs.512227 / Q6ZU74
226582_at / 0.4 / 0.5 / LOC400043 / hypothetical gene supported by BC009385 / 400043 / Hs.19193
202883_s_at / 0.5 / 0.5 / PPP2R1B / protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform / 5519 / Hs.584790 / P30154
39729_at / 0.4 / 0.4 / PRDX2 / peroxiredoxin 2 / 7001 / Hs.432121 / P32119
218683_at / 0.5 / 0.5 / PTBP2 / polypyrimidine tract binding protein 2 / 58155 / Hs.591430 / Q9UKA9
230416_at / 0.1 / 0.4 / SLC18A2 / solute carrier family 18 (vesicular monoamine), member 2 / 6571 / Hs.369009 / Q05940
227062_at / 0.3 / 0.5 / TncRNA / trophoblast-derived noncoding RNA / 283131 / Hs.523789
217729_s_at / 2.1 / 2.0 / AES / amino-terminal enhancer of split / 166 / Hs.515053 / Q08117
209203_s_at / 2.0 / 2.3 / BICD2 / bicaudal D homolog 2 (Drosophila) / 23299 / Hs.436939 / Q8TD16
212702_s_at / 2.5 / 2.7 / BICD2 / bicaudal D homolog 2 (Drosophila) / 23299 / Hs.436939 / Q8TD16
213154_s_at / 2.8 / 2.7 / BICD2 / bicaudal D homolog 2 (Drosophila) / 23299 / Hs.436939 / Q8TD16
225970_at / 2.1 / 2.1 / DDHD1 / DDHD domain containing 1 / 80821 / Hs.513260 / Q8NEL9
201681_s_at / 2.8 / 2.1 / DLG5 / discs, large homolog 5 (Drosophila) / 9231 / Hs.500245 / Q8TDM6
229689_s_at / 2.3 / 2.3 / DLG5 / discs, large homolog 5 (Drosophila) / 9231 / Hs.500245 / Q8TDM6
204646_at / 4.6 / 2.1 / DPYD / dihydropyrimidine dehydrogenase / 1806 / Hs.335034 / Q12882
226811_at / 2.5 / 2.1 / FAM46C / family with sequence similarity 46, member C / 54855 / Hs.356216 / Q5VWP2
212288_at / 2.0 / 2.1 / FNBP1 / formin binding protein 1 / 23048 / Hs.189409 / Q96RU3
209911_x_at / 2.0 / 2.2 / HIST1H2BD / histone cluster 1, H2bd / 3017 / Hs.591797 / P58876
202202_s_at / 4.0 / 2.4 / LAMA4 / laminin, alpha 4 / 3910 / Hs.213861 / Q16363
227940_at / 2.0 / 2.2 / LOC339803 / hypothetical protein LOC339803 / 339803 / Hs.252433
223852_s_at / 2.0 / 2.3 / LSM10 / LSM10, U7 small nuclear RNA associated / 84967 / Hs.471768 / Q969L4
224675_at / 2.3 / 2.0 / MESDC2 / mesoderm development candidate 2 / 23184 / Hs.578450 / Q14696
212473_s_at / 3.1 / 2.3 / MICAL2 / microtubule associated monoxygenase, calponin and LIM domain containing 2 / 9645 / Hs.501928 / O94851
218678_at / 2.8 / 2.0 / NES / nestin / 10763 / Hs.527971 / P48681
226103_at / 3.3 / 2.1 / NEXN / nexilin (F actin binding protein) / 91624 / Hs.632387 / Q0ZGT2
212522_at / 2.2 / 2.1 / PDE8A / phosphodiesterase 8A / 5151 / Hs.9333 / O60658
206157_at / 2.6 / 2.2 / PTX3 / pentraxin-related gene, rapidly induced by IL-1 beta / 5806 / Hs.591286 / P26022
205037_at / 2.3 / 2.2 / RABL4 / RAB, member of RAS oncogene family-like 4 / 11020 / Hs.415172 / Q9BW83
223852_s_at / 2.0 / 2.3 / STK40 / serine/threonine kinase 40 / 83931 / Hs.471768 / Q8N2I9
212112_s_at / 2.0 / 2.1 / STX12 / syntaxin 12 / 23673 / Hs.523855 / Q86Y82
224593_at / 2.3 / 2.4 / ZNF664 / zinc finger protein 664 / 144348 / Hs.524828 / Q3ZCQ7
226562_at / 2.6 / 2.1 / ZNF690 / zinc finger protein 690 / 146050 / Hs.418287 / Q8IWY8

Probe sets listed are altered at least 2-fold downregulated (green) or upregulated (red) compared with the non-specific siRNA experiment in control cells, and were mapped to UniGene, Entrez Gene and SwissProt. Genes/proteins that were matched to protein-protein interactions (PPIs ) in I2Dver. 1.7 appear in boldface in SwissProt ID.

Supplementary Table 2B. List of downregulated and upregulated genes unique to cyclin D1 knockdown

Probe set / Fold change / Gene Symbol / Gene Name / Entrez Gene / UniGene / SwissProt
225707_at / 0.4 / ARL6IP6 / ADP-ribosylation-like factor 6 interacting protein 6 / 151188 / Hs.516468 / Q7Z4G7
225711_at / 0.4 / ARL6IP6 / ADP-ribosylation-like factor 6 interacting protein 6 / 151188 / Hs.516468 / Q7Z4G7
213026_at / 0.4 / ATG12 / ATG12 autophagy related 12 homolog (S. cerevisiae) / 9140 / Hs.264482 / O94817
226785_at / 0.5 / ATP11C / ATPase, Class VI, type 11C / 286410 / Hs.88252 / Q8NB49
223652_at / 0.5 / C10orf32 / chromosome 10 open reading frame 32 / 119032 / Hs.34492 / Q96B45
230364_at / 0.5 / CHPT1 / choline phosphotransferase 1 / 56994 / Hs.293077 / Q8WUD6
225009_at / 0.4 / CMTM4 / CKLF-like MARVEL transmembrane domain containing 4 / 146223 / Hs.643961 / Q8IZR5
222476_at / 0.4 / CNOT6 / CCR4-NOT transcription complex, subunit 6 / 57472 / Hs.157606 / Q9ULM6
204172_at / 0.4 / CPOX / coproporphyrinogen oxidase / 1371 / Hs.476982 / P36551
230426_at / 0.5 / DLD / dihydrolipoamide dehydrogenase / 1738 / Hs.131711 / P09622
228033_at / 0.5 / E2F7 / E2F transcription factor 7 / 144455 / Hs.416375 / Q96AV8
201017_at / 0.5 / EIF1AX / eukaryotic translation initiation factor 1A, X-linked / 1964 / Hs.522590 / O75642
223068_at / 0.5 / EML4 / echinoderm microtubule associated protein like 4 / 27436 / Hs.593614 / Q9HC35
231576_at / 0.5 / ETNK1 / ethanolamine kinase 1 / 55500 / Hs.29464 / Q9HBU6
226965_at / 0.5 / FAM116A / family with sequence similarity 116, member A / 201627 / Hs.91085 / Q8TEG8
235030_at / 0.4 / FAM55C / family with sequence similarity 55, member C / 91775 / Hs.130195 / Q969Y0
235169_at / 0.4 / FBXO27 / F-box protein 27 / 126433 / Hs.187461 / Q8NI29
210950_s_at / 0.5 / FDFT1 / farnesyl-diphosphate farnesyltransferase 1 / 2222 / Hs.593928 / P37268
209864_at / 0.5 / FRAT2 / frequently rearranged in advanced T-cell lymphomas 2 / 23401 / Hs.140720 / O75474
222587_s_at / 0.4 / GALNT7 / UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) / 51809 / Hs.127407 / Q86SF2
218313_s_at / 0.4 / GALNT7 / UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) / 51809 / Hs.127407 / Q86SF2
230278_at / 0.3 / GPR137B / G protein-coupled receptor 137B / 7107 / Hs.498160 / O60478
210148_at / 0.3 / HIPK3 / homeodomain interacting protein kinase 3 / 10114 / Hs.201918 / Q9H422
229667_s_at / 0.4 / HOXB8 / homeobox B8 / 3218 / Hs.514292 / P17481
218091_at / 0.5 / HRB / HIV-1 Rev binding protein / 3267 / Hs.591619 / P52594
208935_s_at / 0.5 / LGALS8 / lectin, galactoside-binding, soluble, 8 (galectin 8) / 3964 / Hs.4082 / O00214
229349_at / 0.4 / LIN28B / lin-28 homolog B (C. elegans) / 389421 / Hs.23616 / Q6ZN17
1559139_at / 0.5 / LOC205251 / LOC205251 / 205251 / Hs.128499 / Q8NCU8
238506_at / 0.4 / LRRC58 / leucine rich repeat containing 58 / 116064 / Hs.518084 / Q96CX6
225479_at / 0.5 / LRRC58 / leucine rich repeat containing 58 / 116064 / Hs.518084 / Q96CX6
224568_x_at / 0.3 / MALAT1 / metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) / 378938 / Hs.642877
223940_x_at / 0.4 / MALAT1 / metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) / 378938 / Hs.642877
1558678_s_at / 0.4 / MALAT1 / metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) / 378938 / Hs.642877
224567_x_at / 0.4 / MALAT1 / metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) / 378938 / Hs.642877
227510_x_at / 0.5 / MALAT1 / metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) / 378938 / Hs.642877
226675_s_at / 0.5 / MALAT1 / metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) / 378938 / Hs.642877
231735_s_at / 0.5 / MALAT1 / metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) / 378938 / Hs.642877
211071_s_at / 0.4 / MLLT11 / myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11 / 10962 / Hs.75823 / Q13015
214078_at / 0.5 / PAK3 / p21 (CDKN1A)-activated kinase 3 / 5063 / Hs.390616 / O75914
213372_at / 0.4 / PAQR3 / progestin and adipoQ receptor family member III / 152559 / Hs.632591 / Q6TCH7
229830_at / 0.4 / PDGFA / platelet-derived growth factor alpha polypeptide / 5154 / Hs.645488 / P04085
225829_at / 0.3 / PDZD8 / PDZ domain containing 8 / 118987 / Hs.501149 / Q8NEN9
225367_at / 0.4 / PGM2 / phosphoglucomutase 2 / 55276 / Hs.23363 / Q96G03
223738_s_at / 0.5 / PGM2 / phosphoglucomutase 2 / 55276 / Hs.23363 / Q96G03
228722_at / 0.4 / PRMT2 / protein arginine methyltransferase 2 / 3275 / Hs.154163 / P55345
218053_at / 0.4 / PRPF40A / PRP40 pre-mRNA processing factor 40 homolog A (yeast) / 55660 / Hs.591637 / O75400
233080_s_at / 0.5 / PRPF40A / PRP40 pre-mRNA processing factor 40 homolog A (yeast) / 55660 / Hs.591637 / O75400
225796_at / 0.5 / PXK / PX domain containing serine/threonine kinase / 54899 / Hs.190544 / Q7Z7A4
228030_at / 0.4 / RBM6 / RNA binding motif protein 6 / 10180 / Hs.596224 / P78332
218793_s_at / 0.4 / SCML1 / sex comb on midleg-like 1 (Drosophila) / 6322 / Hs.109655 / Q9UN30
228026_at / 0.3 / SIKE / suppressor of IKK epsilon / 80143 / Hs.632428 / Q5TEZ9
204666_s_at / 0.4 / SIKE / suppressor of IKK epsilon / 80143 / Hs.632428 / Q5TEZ9
221705_s_at / 0.4 / SIKE / suppressor of IKK epsilon / 80143 / Hs.632428 / Q5TEZ9
212281_s_at / 0.5 / TMEM97 / transmembrane protein 97 / 27346 / Hs.199695 / Q5BJF2
205347_s_at / 0.5 / TMSL8 / thymosin-like 8 / 11013 / Hs.56145 / Q99406
222480_at / 0.5 / UBE2Q1 / ubiquitin-conjugating enzyme E2Q (putative) 1 / 55585 / Hs.607928 / Q7Z7E8
235003_at / 0.3 / UHMK1 / U2AF homology motif (UHM) kinase 1 / 127933 / Hs.127310 / Q8TAS1
1552656_s_at / 0.4 / UHMK1 / U2AF homology motif (UHM) kinase 1 / 127933 / Hs.127310 / Q8TAS1
212388_at / 0.2 / USP24 / ubiquitin specific peptidase 24 / 23358 / Hs.477009 / Q9UPU5
238057_at / 0.5 / USP45 / ubiquitin specific peptidase 45 / 85015 / Hs.143410 / Q70EL2
1557132_at / 0.4 / WDR17 / WD repeat domain 17 / 116966 / Hs.532056 / Q8IZU2
203505_at / 2.2 / ABCA1 / ATP-binding cassette, sub-family A (ABC1), member 1 / 19 / Hs.429294 / O95477
209765_at / 2.1 / ADAM19 / ADAM metallopeptidase domain 19 (meltrin beta) / 8728 / Hs.483944 / Q9H013
204497_at / 2.4 / ADCY9 / adenylate cyclase 9 / 115 / Hs.391860 / O60503
230275_at / 2.4 / ARSI / arylsulfatase family, member I / 340075 / Hs.591252 / Q5FYB1
215037_s_at / 2.1 / BCL2L1 / BCL2-like 1 / 598 / Hs.516966 / Q07817
228434_at / 2.2 / BTNL9 / butyrophilin-like 9 / 153579 / Hs.546502 / Q6UXG8
226487_at / 2.1 / C12orf34 / chromosome 12 open reading frame 34 / 84915 / Hs.144655 / Q5U5X8
219563_at / 2.3 / C14orf139 / chromosome 14 open reading frame 139 / 79686 / Hs.41502 / Q9H761
232235_at / 2.6 / C18orf4 / chromosome 18 open reading frame 4 / 92126 / Hs.124673 / Q8IZU8
243292_at / 2.9 / C1QDC2 / C1q domain containing 2 / 388581 / Hs.197613 / Q5T7M4
225048_at / 2.1 / C6orf120 / chromosome 6 open reading frame 120 / 387263 / Hs.435933 / Q7Z4R8
224370_s_at / 2.1 / CAPS2 / calcyphosine 2 / 84698 / Hs.407154 / Q9BXY5
207181_s_at / 2.1 / CASP7 / caspase 7, apoptosis-related cysteine peptidase / 840 / Hs.9216 / P55210
211922_s_at / 2.3 / CAT / catalase / 847 / Hs.502302 / P04040
201432_at / 2.1 / CAT / catalase / 847 / Hs.502302 / P04040
201925_s_at / 2.2 / CD55 / CD55 molecule, decay accelerating factor for complement (Cromer blood group) / 1604 / Hs.527653 / P08174
228748_at / 2.5 / CD59 / CD59 molecule, complement regulatory protein / 966 / Hs.278573 / P13987
209288_s_at / 2.3 / CDC42EP3 / CDC42 effector protein (Rho GTPase binding) 3 / 10602 / Hs.369574 / Q9UKI2
209286_at / 2.1 / CDC42EP3 / CDC42 effector protein (Rho GTPase binding) 3 / 10602 / Hs.369574 / Q9UKI2
235443_at / 2.7 / CKMT2 / creatine kinase, mitochondrial 2 (sarcomeric) / 1160 / Hs.80691 / P17540
218182_s_at / 2.3 / CLDN1 / claudin 1 / 9076 / Hs.439060 / O95832
229271_x_at / 3.6 / COL11A1 / collagen, type XI, alpha 1 / 1301 / Hs.523446 / P12107
37892_at / 2.8 / COL11A1 / collagen, type XI, alpha 1 / 1301 / Hs.523446 / P12107
204320_at / 2.2 / COL11A1 / collagen, type XI, alpha 1 / 1301 / Hs.523446 / P12107
206100_at / 3.0 / CPM / carboxypeptidase M / 1368 / Hs.484551 / P14384
227473_at / 2.1 / CTTN / cortactin / 2017 / Hs.632133 / Q14247
214743_at / 2.1 / CUTL1 / cut-like 1, CCAAT displacement protein (Drosophila) / 1523 / Hs.191482 / P39880
234915_s_at / 2.3 / DENR / density-regulated protein / 8562 / Hs.22393 / O43583
221509_at / 2.2 / DENR / density-regulated protein / 8562 / Hs.22393 / O43583
231896_s_at / 2.1 / DENR / density-regulated protein / 8562 / Hs.22393 / O43583
218995_s_at / 2.1 / EDN1 / endothelin 1 / 1906 / Hs.621232 / P05305
204797_s_at / 2.2 / EML1 / echinoderm microtubule associated protein like 1 / 2009 / Hs.12451 / O00423
238533_at / 2.0 / EPHA7 / EPH receptor A7 / 2045 / Hs.73962 / Q15375
201889_at / 2.6 / FAM3C / family with sequence similarity 3, member C / 10447 / Hs.434053 / Q92520
225864_at / 3.3 / FAM84B / family with sequence similarity 84, member B / 157638 / Hs.124951 / Q96KN1
204359_at / 2.1 / FLRT2 / fibronectin leucine rich transmembrane protein 2 / 23768 / Hs.533710 / O43155
225481_at / 2.3 / FRMD6 / FERM domain containing 6 / 122786 / Hs.434914 / Q96NE9
225464_at / 2.1 / FRMD6 / FERM domain containing 6 / 122786 / Hs.434914 / Q96NE9
229441_at / 2.0 / FZD4 / frizzled homolog 4 (Drosophila) / 8322 / Hs.591968 / Q9ULV1
208841_s_at / 2.3 / G3BP2 / GTPase activating protein (SH3 domain) binding protein 2 / 9908 / Hs.303676 / Q9UN86
223278_at / 3.9 / GJB2 / gap junction protein, beta 2, 26kDa (connexin 26) / 2706 / Hs.591234 / P29033
231771_at / 3.0 / GJB6 / gap junction protein, beta 6 (connexin 30) / 10804 / Hs.511757 / O95452
221869_at / 2.4 / GM632 / KIAA1196 protein / 57473 / Hs.551552 / Q96KM6
224646_x_at / 2.2 / H19 / H19, imprinted maternally expressed untranslated mRNA / 283120 / Hs.533566
223541_at / 2.6 / HAS3 / hyaluronan synthase 3 / 3038 / Hs.592069 / O00219
202815_s_at / 2.1 / HEXIM1 / hexamethylene bis-acetamide inducible 1 / 10614 / Hs.15299 / O94992
211538_s_at / 2.4 / HSPA2 / heat shock 70kDa protein 2 / 3306 / Hs.432648 / P54652
201466_s_at / 2.4 / JUN / jun oncogene / 3725 / Hs.525704 / P05412
224392_s_at / 3.8 / KMO / kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) / 8564 / Hs.409081 / O15229
219032_x_at / 3.5 / KMO / kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) / 8564 / Hs.409081 / O15229
204734_at / 3.0 / KRT15 / keratin 15 / 3866 / Hs.2785 / P19012
235497_at / 2.0 / LOC643837 / hypothetical protein LOC643837 / 643837 / Hs.593676 / Q96BN7
225540_at / 3.1 / LOC648149 / hypothetical protein LOC648149 / 648149 / Hs.368281 / Q6ZWB4
225540_at / 3.1 / MAP2 / microtubule-associated protein 2 / 4133 / Hs.368281 / P11137
218181_s_at / 2.2 / MAP4K4 / mitogen-activated protein kinase kinase kinase kinase 4 / 9448 / Hs.431550 / O95819
226487_at / 2.1 / MGC14436 / hypothetical protein MGC14436 / 84983 / Hs.144655 / Q96I53
206100_at / 3.0 / MGC5370 / hypothetical protein MGC5370 / 84825 / Hs.484551
211026_s_at / 2.7 / MGLL / monoglyceride lipase / 11343 / Hs.277035 / Q99685
225782_at / 2.0 / MSRB3 / methionine sulfoxide reductase B3 / 253827 / Hs.339024 / Q6UXS2
214156_at / 2.0 / MYRIP / myosin VIIA and Rab interacting protein / 25924 / Hs.594535 / Q8NFW9
229461_x_at / 8.8 / NEGR1 / neuronal growth regulator 1 / 257194 / Hs.146542 / Q7Z3B1
243357_at / 2.3 / NEGR1 / neuronal growth regulator 1 / 257194 / Hs.146542 / Q7Z3B1
242539_at / 2.0 / NRBF2 / nuclear receptor binding factor 2 / 29982 / Hs.449628 / Q96F24
224392_s_at / 3.8 / OPN3 / opsin 3 (encephalopsin, panopsin) / 23596 / Hs.409081 / Q9H1Y3
219032_x_at / 3.5 / OPN3 / opsin 3 (encephalopsin, panopsin) / 23596 / Hs.409081 / Q9H1Y3
232054_at / 2.8 / PCDH20 / protocadherin 20 / 64881 / Hs.391781 / Q8N6Y1
229256_at / 2.8 / PGM2L1 / phosphoglucomutase 2-like 1 / 283209 / Hs.26612 / Q6PCE3
229553_at / 2.4 / PGM2L1 / phosphoglucomutase 2-like 1 / 283209 / Hs.26612 / Q6PCE3
238417_at / 2.4 / PGM2L1 / phosphoglucomutase 2-like 1 / 283209 / Hs.26612 / Q6PCE3
225048_at / 2.1 / PHF10 / PHD finger protein 10 / 55274 / Hs.435933 / Q8WUB8
221538_s_at / 2.7 / PLXNA1 / plexin A1 / 5361 / Hs.432329 / Q9UIW2
201578_at / 3.3 / PODXL / podocalyxin-like / 5420 / Hs.16426 / O00592
217944_at / 2.0 / POMGNT1 / protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase / 55624 / Hs.525134 / Q8WZA1
209529_at / 2.1 / PPAP2C / phosphatidic acid phosphatase type 2C / 8612 / Hs.465506 / O43688
203355_s_at / 2.3 / PSD3 / pleckstrin and Sec7 domain containing 3 / 23362 / Hs.434255 / Q9NYI0
210355_at / 2.2 / PTHLH / parathyroid hormone-like hormone / 5744 / Hs.591159 / P12272
208300_at / 2.1 / PTPRH / protein tyrosine phosphatase, receptor type, H / 5794 / Hs.179770 / Q15426
238447_at / 2.3 / RBMS3 / RNA binding motif, single stranded interacting protein / 27303 / Hs.696468 / Q6XE24
202388_at / 2.8 / RGS2 / regulator of G-protein signalling 2, 24kDa / 5997 / Hs.78944 / P41220
201204_s_at / 2.2 / RRBP1 / ribosome binding protein 1 homolog 180kDa (dog) / 6238 / Hs.472213 / Q9P2E9
202627_s_at / 2.3 / SERPINE1 / serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 / 5054 / Hs.414795 / P05121
201739_at / 2.3 / SGK / serum/glucocorticoid regulated kinase / 6446 / Hs.510078 / O00141
235050_at / 2.1 / SLC2A12 / solute carrier family 2 (facilitated glucose transporter), member 12 / 154091 / Hs.486508 / Q8TD20
232481_s_at / 2.5 / SLITRK6 / SLIT and NTRK-like family, member 6 / 84189 / Hs.525105 / Q9H5Y7
212956_at / 2.3 / TBC1D9 / TBC1 domain family, member 9 (with GRAM domain) / 23158 / Hs.480819 / O94958
201042_at / 2.0 / TGM2 / transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase) / 7052 / Hs.517033 / P21980
201110_s_at / 5.2 / THBS1 / thrombospondin 1 / 7057 / Hs.164226 / P07996
201109_s_at / 3.4 / THBS1 / thrombospondin 1 / 7057 / Hs.164226 / P07996
211689_s_at / 2.8 / TMPRSS2 / transmembrane protease, serine 2 / 7113 / Hs.439309 / O15393
210986_s_at / 2.1 / TPM1 / tropomyosin 1 (alpha) / 7168 / Hs.133892 / P09493
210987_x_at / 2.1 / TPM1 / tropomyosin 1 (alpha) / 7168 / Hs.133892 / P09493
221571_at / 2.3 / TRAF3 / TNF receptor-associated factor 3 / 7187 / Hs.510528 / Q13114
215111_s_at / 2.1 / TSC22D1 / TSC22 domain family, member 1 / 8848 / Hs.507916 / Q15714
55872_at / 2.6 / UCKL1 / uridine-cytidine kinase 1-like 1 / 54963 / Hs.504998 / Q9NWZ5
211009_s_at / 2.1 / ZNF271 / zinc finger protein 271 / 10778 / Hs.314246 / Q14591
206557_at / 2.7 / ZNF320 / zinc finger protein 320 / 162967 / Hs.467223 / Q6ZP55
214751_at / 2.2 / ZNF320 / zinc finger protein 320 / 162967 / Hs.467223 / Q6ZP55
206557_at / 2.7 / ZNF468 / zinc finger protein 468 / 90333 / Hs.467223 / Q5CZB8
214751_at / 2.2 / ZNF468 / zinc finger protein 468 / 90333 / Hs.467223 / Q5CZB8
204453_at / 2.1 / ZNF84 / zinc finger protein 84 / 7637 / Hs.445019 / P51523

Probe sets listed are altered at least 2-fold downregulated (green) or upregulated (red) compared to the non-specific siRNA experiment in control cells, and were mapped to UniGene, Entrez Gene and SwissProt. Genes/proteins that were matched to protein-protein interactions (PPIs) in I2Dver. 1.7 appear in boldface in SwissProt ID.

Supplementary Table 2C. List of downregulated and upregulated genes unique to cyclin D3 knockdown

Probe set / Fold change / Gene Symbol / Gene Name / Entrez Gene / UniGene / SwissProt
1552287_s_at / 0.5 / AFG3L1 / AFG3 ATPase family gene 3-like 1 (S. cerevisiae) / 172 / Hs.534773 / O43931
221505_at / 0.5 / ANP32E / acidic (leucine-rich) nuclear phosphoprotein 32 family, member E / 81611 / Hs.603000 / Q9BTT0
229128_s_at / 0.5 / ANP32E / acidic (leucine-rich) nuclear phosphoprotein 32 family, member E / 81611 / Hs.603000 / Q9BTT0
200761_s_at / 0.5 / ARL6IP5 / ADP-ribosylation-like factor 6 interacting protein 5 / 10550 / Hs.518060 / O75915
203487_s_at / 0.5 / ARMC8 / armadillo repeat containing 8 / 25852 / Hs.266826 / Q6PIL2
226517_at / 0.5 / BCAT1 / branched chain aminotransferase 1, cytosolic / 586 / Hs.438993 / P54687
224367_at / 0.5 / BEX2 / brain expressed X-linked 2 / 84707 / Hs.398989 / Q9BXY8
224719_s_at / 0.5 / C12orf57 / chromosome 12 open reading frame 57 / 113246 / Hs.591045 / Q99622
218940_at / 0.4 / C14orf138 / chromosome 14 open reading frame 138 / 79609 / Hs.558541 / Q9H867
239038_at / 0.4 / C1orf52 / chromosome 1 open reading frame 52 / 148423 / Hs.26226 / Q8N6N3
227627_at / 0.5 / C8orf44 / chromosome 8 open reading frame 44 / 56260 / Hs.545401 / Q96CB5
202284_s_at / 0.5 / CDKN1A / cyclin-dependent kinase inhibitor 1A (p21, Cip1) / 1026 / Hs.370771 / P38936
205474_at / 0.4 / CRLF3 / cytokine receptor-like factor 3 / 51379 / Hs.370168 / Q8IUI8
201372_s_at / 0.5 / CUL3 / cullin 3 / 8452 / Hs.372286 / Q13618
219825_at / 0.4 / CYP26B1 / cytochrome P450, family 26, subfamily B, polypeptide 1 / 56603 / Hs.91546 / Q9NR63
204244_s_at / 0.4 / DBF4 / DBF4 homolog (S. cerevisiae) / 10926 / Hs.485380 / Q9UBU7
218277_s_at / 0.4 / DHX40 / DEAH (Asp-Glu-Ala-His) box polypeptide 40 / 79665 / Hs.29403 / Q8IX18
224215_s_at / 0.5 / DLL1 / delta-like 1 (Drosophila) / 28514 / Hs.379912 / O00548
222692_s_at / 0.5 / FNDC3B / fibronectin type III domain containing 3B / 64778 / Hs.159430 / Q53EP0
222693_at / 0.4 / FNDC3B / fibronectin type III domain containing 3B / 64778 / Hs.159430 / Q53EP0
211458_s_at / 0.5 / GABARAPL3 / GABA(A) receptors associated protein like 3 / 23766 / Hs.592014 / Q9BY60
207574_s_at / 0.4 / GADD45B / growth arrest and DNA-damage-inducible, beta / 4616 / Hs.110571 / O75293
209304_x_at / 0.5 / GADD45B / growth arrest and DNA-damage-inducible, beta / 4616 / Hs.110571 / O75293
231871_at / 0.4 / GPR180 / G protein-coupled receptor 180 / 160897 / Hs.439363 / Q86V85
203632_s_at / 0.5 / GPRC5B / G protein-coupled receptor, family C, group 5, member B / 51704 / Hs.148685 / Q9NZH0
207002_s_at / 0.5 / HYMAI / hydatidiform mole associated and imprinted / 57061 / Hs.444975
219209_at / 0.5 / IFIH1 / interferon induced with helicase C domain 1 / 64135 / Hs.163173 / Q9BYX4
226757_at / 0.5 / IFIT2 / interferon-induced protein with tetratricopeptide repeats 2 / 3433 / Hs.437609 / P09913
225511_at / 0.5 / IQCK / IQ motif containing K / 124152 / Hs.460217 / Q8N0W5
219479_at / 0.5 / KDELC1 / KDEL (Lys-Asp-Glu-Leu) containing 1 / 79070 / Hs.408629 / Q6UW63
223800_s_at / 0.4 / LIMS3 / LIM and senescent cell antigen-like domains 3 / 96626 / Hs.535619 / Q9HB10
231871_at / 0.4 / LOC144874 / hypothetical protein LOC144874 / 144874 / Hs.439363
223800_s_at / 0.4 / LOC440895 / similar to LIM and senescent cell antigen-like domains 3 / 440895 / Hs.535619
228423_at / 0.5 / MAP9 / microtubule-associated protein 9 / 79884 / Hs.61271 / Q49MG5
227379_at / 0.5 / MBOAT1 / membrane bound O-acyltransferase domain containing 1 / 154141 / Hs.377830 / Q6ZNC8
202731_at / 0.5 / PDCD4 / programmed cell death 4 (neoplastic transformation inhibitor) / 27250 / Hs.232543 / Q53EL6
212593_s_at / 0.4 / PDCD4 / programmed cell death 4 (neoplastic transformation inhibitor) / 27250 / Hs.232543 / Q53EL6
207002_s_at / 0.5 / PLAGL1 / pleiomorphic adenoma gene-like 1 / 5325 / Hs.444975 / Q9UM63
201375_s_at / 0.4 / PPP2CB / protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform / 5516 / Hs.491440 / P62714
227627_at / 0.5 / PTTG3 / pituitary tumor-transforming 3 / 26255 / Hs.545401 / O95356
209515_s_at / 0.4 / RAB27A / RAB27A, member RAS oncogene family / 5873 / Hs.493512 / P51159
227369_at / 0.5 / SERBP1 / SERPINE1 mRNA binding protein 1 / 26135 / Hs.530412 / Q8NC51
227627_at / 0.5 / SGK3 / serum/glucocorticoid regulated kinase family, member 3 / 23678 / Hs.545401 / Q96BR1
210567_s_at / 0.5 / SKP2 / S-phase kinase-associated protein 2 (p45) / 6502 / Hs.23348 / Q13309
229065_at / 0.4 / SLC35F3 / solute carrier family 35, member F3 / 148641 / Hs.158748 / Q8N9C9
1555460_a_at / 0.5 / SLC39A6 / solute carrier family 39 (zinc transporter), member 6 / 25800 / Hs.79136 / Q13433
202089_s_at / 0.4 / SLC39A6 / solute carrier family 39 (zinc transporter), member 6 / 25800 / Hs.79136 / Q13433
209198_s_at / 0.4 / SYT11 / synaptotagmin XI / 23208 / Hs.32984 / Q9BT88
201448_at / 0.5 / TIA1 / TIA1 cytotoxic granule-associated RNA binding protein / 7072 / Hs.516075 / P31483
227459_at / 0.4 / TMEM140 / transmembrane protein 140 / 55281 / Hs.567530 / Q8WUC3
228029_at / 2.2 / ABCA11 / ATP-binding cassette, sub-family A (ABC1), member 11 (pseudogene) / 79963 / Hs.428360 / Q4W5N1
201284_s_at / 2.0 / APEH / N-acylaminoacyl-peptide hydrolase / 327 / Hs.517969 / P13798
212423_at / 2.1 / C10orf56 / chromosome 10 open reading frame 56 / 219654 / Hs.523080 / Q5U5T9
233543_s_at / 2.1 / CCDC98 / coiled-coil domain containing 98 / 84142 / Hs.334772 / Q6UWZ7
235287_at / 2.0 / CDK6 / cyclin-dependent kinase 6 / 1021 / Hs.119882 / Q00534
211934_x_at / 2.2 / GANAB / glucosidase, alpha; neutral AB / 23193 / Hs.595071 / Q14697
214626_s_at / 2.2 / GANAB / glucosidase, alpha; neutral AB / 23193 / Hs.595071 / Q14697
212355_at / 2.2 / KIAA0323 / KIAA0323 / 23351 / Hs.643552 / O15037
228029_at / 2.2 / LOC152719 / hypothetical protein LOC152719 / 152719 / Hs.428360
238437_at / 2.1 / LOC390980 / similar to Zinc finger protein 264 / 390980 / Hs.22488 / Q5CZA5
207098_s_at / 2.0 / MFN1 / mitofusin 1 / 55669 / Hs.478383 / Q8IWA4
232028_at / 2.0 / MGC15634 / hypothetical protein MGC15634 / 84841 / Hs.30323
218951_s_at / 2.1 / PLCXD1 / phosphatidylinositol-specific phospholipase C, X domain containing 1 / 55344 / Hs.522568 / Q9NUJ7
212561_at / 2.1 / RAB6IP1 / RAB6 interacting protein 1 / 23258 / Hs.501857 / Q6IQ26
205485_at / 2.2 / RYR1 / ryanodine receptor 1 (skeletal) / 6261 / Hs.466664 / P21817
224928_at / 2.3 / SETD7 / SET domain containing (lysine methyltransferase) 7 / 80854 / Hs.480792 / Q8WTS6
210664_s_at / 2.1 / TFPI / tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) / 7035 / Hs.516578 / P10646
221255_s_at / 2.0 / TMEM93 / transmembrane protein 93 / 83460 / Hs.30011 / Q9BV81
244551_at / 2.0 / TRIM60 / tripartite motif-containing 60 / 166655 / Hs.368004 / Q495X7
210276_s_at / 2.5 / TRIOBP / TRIO and F-actin binding protein / 11078 / Hs.533030 / Q9H2D6
216210_x_at / 2.1 / TRIOBP / TRIO and F-actin binding protein / 11078 / Hs.533030 / Q9H2D6
203597_s_at / 2.1 / WBP4 / WW domain binding protein 4 (formin binding protein 21) / 11193 / Hs.411300 / O75554
219540_at / 2.4 / ZNF267 / zinc finger protein 267 / 10308 / Hs.460645 / Q14586
1558722_at / 2.2 / ZNF454 / zinc finger protein 454 / 285676 / Hs.259441 / Q8N9F8
232028_at / 2.0 / ZNF678 / zinc finger protein 678 / 339500 / Hs.30323 / Q5SXM1
229533_x_at / 2.0 / ZNF680 / zinc finger protein 680 / 340252 / Hs.520886 / Q8NEM1
239482_x_at / 2.1 / ZNF708 / zinc finger protein 708 / 7562 / Hs.466296 / P17019
228029_at / 2.2 / ZNF721 / zinc finger protein 721 / 170960 / Hs.428360 / Q8TF20
206059_at / 2.0 / ZNF91 / zinc finger protein 91 / 7644 / Hs.631626 / Q05481